porousmedialab 3.0.0

Toolbox for batch and 1D reactive transport modeling in porous media aimed on easiness of use for the user without computational background

PorousMediaLab

The toolbox for batch and 1D reactive transport modelling in porous media aimed at the easiness of use for the user without computational background.

What's New in v2.2.0

Robustness and maintainability improvements with expanded test coverage:

• Input validation across the solver: division-by-zero guards and a CFL stability warning catch unstable grids early
• Behavior-preserving refactor of the core ODE/PDE solver and class contracts (boundary conditions, flux estimators, acid-base updates)
• Removed unused code (sensitivity.py stubs, dead element.py, legacy Python 2 compatibility)
• Test suite expanded to 389 tests, including mathematical-correctness integration tests

What's New in v2.1.1

Correctness and packaging hardening for solver setup and release artifacts:

• Validates time and spatial grids to prevent silently shifted dt and dx
• Fixes ODE derivative ordering, Batch solver dispatch, flux estimators, and calibration depth comparisons
• Removes obsolete binary build artifacts and legacy upload scripts from the source distribution

What's New in v2.1.0

2.4x overall performance improvement with optimized rate reconstruction:

• Vectorized reconstruct_rates() method - 45x faster
• Enabled numexpr multi-threading for parallel rate expression evaluation
• Pre-allocated arrays in hot loops to reduce memory overhead

What's New in v2.0.0

6-60x faster reaction integration with the new vectorized ODE solver:

• Reactions are now solved using a vectorized approach that processes all spatial points simultaneously
• Uses scipy.integrate.solve_ivp with LSODA method (auto-detects stiffness)
• Backward compatible: use ode_method='scipy_sequential' for the old behavior

Spatial Points	Species	Speedup
50	2	13x
100	3	23x
500	5	62x

How to use

Have a look at "examples" folder.

Installation using pip

• Install Python version 3.10 or higher (click);
• To install the toolbox run pip install porousmedialab
• In terminal run jupyter notebook;
• You will see the folders in your home folder. You can navigate in any folder and create a new notebook with your model.

Development installation using Poetry

• Install Python version 3.10 or higher (click);
• Install Poetry (click);
• Clone this repository: git clone https://github.com/biogeochemistry/PorousMediaLab
• Navigate to the project folder: cd PorousMediaLab
• Install dependencies: poetry install
• Run tests: poetry run pytest
• Activate the virtual environment: poetry shell

Development Commands (Makefile)

The project includes a Makefile for common tasks:

make install       # Install dependencies
make test          # Run test suite
make benchmark     # Run performance optimization benchmark
make benchmark-ode # Run ODE solver benchmark
make build         # Build package
make publish       # Publish to PyPI
make release       # Build and publish
make clean         # Clean build artifacts

Manual installation

• Install Python version 3.10 or higher (click);
• Download and unzip or clone (using git) this repository (PorousMediaLab);
• Open terminal and go to the PorousMediaLab folder using cd command. If you have problems with the terminal, check this guide;
• Install dependencies: pip install numpy numexpr scipy matplotlib seaborn h5py scikit-learn
• In terminal run command jupyter notebook;
• You will see the folders of the PorousMediaLab project; you can go in "examples" folder and play with them.

Testing

To run the test suite:

pip install pytest pytest-cov
pytest tests/ -v

For coverage report:

pytest tests/ --cov=porousmedialab --cov-report=term-missing

Citation

Igor Markelov (2020). Modelling Biogeochemical Cycles Across Scales: From Whole-Lake Phosphorus Dynamics to Microbial Reaction Systems. UWSpace. http://hdl.handle.net/10012/15513

Contribution

I am looking for contributors specifically for incorporation of:

• sensitivity tests
• unsaturated flow
• thermodynamic calculations
• your crazy ideas and needs

If you wish to contribute in this open source project, please, create pull request or contact me via email: [e-mail].

Acknowledgements

This project was funded by

• Lakes in Transition (Research Council of Norway project no. 244558/E50 (https://prosjektbanken.forskningsradet.no/#/project/NFR/244558)

• the Canada Excellence Research Chair in Ecohydrology (https://www.cerc.gc.ca/chairholders-titulaires/former-ancien-eng.aspx).

MIT License

Copyright (c) 2019 Igor Markelov

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.